The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO2 and N2O direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct N2O emissions when treated with agricultural wastes. The highest soil direct N2O emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct N2O emissions. On the contrary, agricultural wastes stimulated CO2 accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil N2O emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with N2O emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced N2O emissions.